Changing CLI

.gitignore

@@ -18,3 +18,4 @@ tests/tmp_results_folder/*
 pathopatch.egg-info/
 dist
 build
+push_build.yml

examples/patch_extraction.yaml

@@ -77,3 +77,4 @@ log_path:                     # Path where log files should be stored. Otherwise
 log_level:                    # Set the logging level. [str][Optional, defaults to info]
 hardware_selection:           # Select hardware device (just if available, otherwise always cucim). [str] [Optional, defaults to cucim]
 wsi_properties:               # Dictionary with manual WSI metadata. Required keys are: ... TODO: add keys [dict] [Optional, default selection from files]
+# TODO: Change WSI properties to mpp and magnification

pathopatch/cli.py

@@ -577,9 +577,14 @@ def __init__(self) -> None:
             help="Select hardware device (just if available, otherwise always cucim). Defaults to cucim.",
         )
         parser.add_argument(
-            "--wsi_properties",
-            type=dict,
-            help="Dictionary with manual WSI metadata, but just applies if metadata cannot be derived from OpenSlide (e.g., for .tiff files). Supported keys are slide_mpp and magnification",
+            "--wsi_magnification",
+            type=float,
+            help="Manual WSI magnification, but just applies if metadata cannot be derived from OpenSlide (e.g., for .tiff files).",
+        )
+        parser.add_argument(
+            "--wsi_mpp",
+            type=float,
+            help="Manual WSI MPP, but just applies if metadata cannot be derived from OpenSlide (e.g., for .tiff files).",
         )
 
         self.parser = parser
@@ -608,6 +613,16 @@ def get_config(self) -> Tuple[PreProcessingConfig, logging.Logger]:
                 raise ValueError("Please provide config file as `.yaml` file")
             with open(opt.config, "r") as config_file:
                 yaml_config = yaml.safe_load(config_file)
+                if "wsi_magnification" in yaml_config or "wsi_mpp" in yaml_config:
+                    yaml_config["wsi_properties"] = {}
+                if "wsi_magnification" in yaml_config:
+                    yaml_config["wsi_properties"]["magnification"] = yaml_config[
+                        "wsi_magnification"
+                    ]
+                    yaml_config.pop("wsi_magnification")
+                if "wsi_mpp" in yaml_config:
+                    yaml_config["wsi_properties"]["slide_mpp"] = yaml_config["wsi_mpp"]
+                    yaml_config.pop("wsi_mpp")
                 yaml_config = PreProcessingYamlConfig(**yaml_config)
 
                 # convert to dict and override missing values
@@ -622,6 +637,16 @@ def get_config(self) -> Tuple[PreProcessingConfig, logging.Logger]:
         else:
             opt_dict = vars(opt)
             opt_dict = {k: v for k, v in opt_dict.items() if v is not None}
+            if "wsi_magnification" in opt_dict or "wsi_mpp" in opt_dict:
+                opt_dict["wsi_properties"] = {}
+            if "wsi_magnification" in opt_dict:
+                opt_dict["wsi_properties"]["magnification"] = opt_dict[
+                    "wsi_magnification"
+                ]
+                opt_dict.pop("wsi_magnification")
+            if "wsi_mpp" in opt_dict:
+                opt_dict["wsi_properties"]["slide_mpp"] = opt_dict["wsi_mpp"]
+                opt_dict.pop("wsi_mpp")
 
         # generate final setup
         self.preprocessconfig = PreProcessingConfig(**opt_dict)

pathopatch/wsi_extraction.py

@@ -10,10 +10,10 @@
 import sys
 import os
 
-# project_root = os.path.dirname(os.path.abspath(__file__))
-# sys.path.append(project_root)
-# project_root = os.path.dirname(os.path.abspath(project_root))
-# sys.path.append(project_root)
+project_root = os.path.dirname(os.path.abspath(__file__))
+sys.path.append(project_root)
+project_root = os.path.dirname(os.path.abspath(project_root))
+sys.path.append(project_root)
 
 import logging